Dannon Baker wrote:
> The 'step' in question is the actual workflow step id, since ordering of
> steps in a workflow is flexible and might be changed without realizing it by
> moving steps around in the editor. The easiest way to retrieve this
> identifier is to use the API and view the workflo
Roxanne Tapia wrote:
> Is there a way to create/view histories via the api, and to associate data in
> libraries to histories?
> Then to share the histories or make them public, and build a URL to view the
> history?
Hi Roxanne.
To the first three, yes. This was added in the most recent stab
Roxanne Tapia wrote:
> Hi,
>
> I was going through the examples in the README, and everything went along
> fine until I tried to upload files from the import directory:
>
> usage: library_upload_from_import_dir.py key url folder_id file_type
> server_dir dbkey
>
> I don't understand what the
Peter Cock wrote:
> On Tue, Sep 6, 2011 at 5:00 PM, Nate Coraor wrote:
> > Peter Cock wrote:
> >> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
> >> > Ideally, there'd just be a column on the dataset table indicating
> >> > whether the dataset
Peter Cock wrote:
> On Tue, Sep 6, 2011 at 3:24 PM, Nate Coraor wrote:
> > Edward Kirton wrote:
> >> Peter wrote:
> >> > I wonder if Galaxy would benefit from a new fastqsanger-gzip (etc)
> >> > datatype?
> >> > However this seems generally
SHAUN WEBB wrote:
>
> Hi.
>
> I am interested in putting quotas in to effect on our local Galaxy
> server. From the admin page I can create a quota but this only seems
> to apply to disk space. I noticed on your test site you have quotas
> for concurrent jobs also. Have I missed how to set this o
Timothy Wu wrote:
> Hi,
>
> I'm trying the add tool tutorial at
> http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but
> how do I designate the path of the tool if it's not dropped into the same
> directory as the tool config xml? Some executable may not be in the
> director
Kristen Eisenberg wrote:
> [galaxy-dev] Failure to prepare job error
>
>
>
> Hello,
>
> I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
> import a package I've installed called PypeR. My tool works fine from the
> command line, but when I try to run it on my Amazon insta
Nikhil Joshi wrote:
> Hi all,
>
> Is there a repository of pre-indexed genomes for base-space/color-space,
> bwa, bam, sam, etc...? It would be much easier than having to index them
> all ourselves :)
Hi Nik,
I've been meaning to set this up for a while now. Stay tuned for an
announcement
Shantanu Pavgi wrote:
>
> Thanks for the reply Kanwei. Is there any announcement or news feed that
> people can subscribe to know when main galaxy instance is updated. This will
> help sites which want to keep up with the PSU's main galaxy instance. Do you
> announce it on the galaxy-user list
ysam
> Fetch failed.
> [~/galaxy-dist] myuserid 03:06 PM >
Could you report back with the output of:
% python ./scripts/get_platforms.py
?
Thanks,
--nate
>
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: Friday, September 02, 2011 1:16
x27;t duplicate this. Is it with a specific file type (and are
you setting the file type explicitly, or using auto-detection)?
> Where can i find the dataset class ?
The datatypes are defined in galaxy-dist/lib/galaxy/datatypes/
--nate
>
> Perhaps, the operation does not work and the
uld make your own copy
with modifications). Also, as outlined above, changes in run.sh are not
propogated to the nodes when running on a cluster.
--nate
>
> best,
> joe
>
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: Friday, September
Edward Kirton wrote:
> > In your position I agree that is a pragmatic choice.
>
> Thanks for helping me muddle through my options.
>
> > You might be able to
> > modify the file upload code to gzip any FASTQ files... that would prevent
> > uncompressed FASTQ getting into new histories.
>
> Right
Chorny, Ilya wrote:
> Nate,
>
> We ran into this issue with /tmp not having enough space. We came up with a
> generic solution and were wondering if you might want to add it to
> galaxy-central. We did not want to modify SGE as it could affect other jobs
> that use the cluster.
>
> We create
Trevor Wennblom wrote:
>
> On Sep 2, 2011, at 1:16 PM, Nate Coraor wrote:
>
> > We haven't yet gotten our dependencies up to speed on Lion. Could you
> > grab a copy of Python from python.org and use this? It'll install under
> > /Library/Frameworks/Pytho
Whyte, Jeffrey wrote:
> Hi,
>
> I've been having trouble running a local instance of Galaxy on a Mac Pro
> after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and
> Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed.
>
> The error I see after running the star
remy d1 wrote:
> Hi,
>
> We found a little problem in the new galaxy release. When we upload a
> dataset library from filesystem :
>
> Admin > Manage data libraries > create new data library > Add dataset >
> Upload files from filesystem path > Link to files without copying
>
> If galaxy user is
Hi Nikolai,
It's best to send questions directly to the mailing list, so they reach
the widest audience and the right people.
There are some responses below:
Nikolai Vazov wrote:
>
> Hi, Nate,
>
> You helped me install Galaxy with a DB hosted on a remote server via
> SSL connection. Thanks a l
IT Support wrote:
> Greetings,
>
> I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to
> a location commonly accessible by all analysis nodes. I then set the path to
> Python 2.7 like so:
>
> export PATH=/opt/galaxy-python/python:$PATH
>
> However, executing run.sh gi
Joseph Hargitai wrote:
> additional info:
>
> it is possible on the same node to run manually
>
> ./gsummary.py
>
> with the header:
>
> #!/usr/bin/env python
>
> import sys, re, tempfile
> from rpy_options import set_options
> set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R')
> from rpy impo
Fields, Christopher J wrote:
> On Sep 2, 2011, at 9:57 AM, Nate Coraor wrote:
>
> > ...
> >> Chatting to some of the Galaxy team at BOSC/ISMB 2011
> >> there is some support for this internally. Again, there are
> >> automated tools to do this.
> &g
Peter Cock wrote:
> On Thu, Sep 1, 2011 at 9:00 PM, Trevor Wennblom wrote:
> > ...
> > given that python has syntactically significant whitespace, i also
> > try to maintain the convention of indentation with four-spaces.
> > i've noticed this isn't consistent within the codebase, but does
> > se
Edward Kirton wrote:
> hi, we are getting the following error migrating from 79 to 80.
> curiously, my own galaxy didn't have this problem, but another
> developer here was getting this error. i moved him from sqlite to
> postgres but that didn't help.
> thanks for any assistance,
> ed
Hi Ed,
Is
Wei,Xintao wrote:
> Hi,
>
> I am learning how to install and configure Galaxy on our computer cluster.
> Many third party tools, for example, bowtie, samtools, R and so on, have to
> be installed and configured in order to install galaxy. Do I have to convert
> the third party tools to MPI ver
Louise-Amélie Schmitt wrote:
> Hello everyone,
>
> I'm currently trying to automate data loading and pre-processing
> through Galaxy's API, and I will need to delete and share histories
> at some point. I know the API is still very new but is there a way
> to do that by any chance?
Hi L-A,
As of
Sarah Diehl wrote:
> I just also found out about this bug (or feature). It is exactly the
> same for me and I'm running an older Galaxy version (galaxy-dist
> from April 8, 2011).
Hi Sarah, Alex,
Dannon fixed this bug back in July, in changeset 5814:ebb1014b237d,
which is now available in galaxy-
Louise-Amélie Schmitt wrote:
> Le 30/08/2011 16:51, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>I just changed it and ran into an error, so I modified the line and
> >>it now works fine:
> >>$__app__.security.encode_id( '%s' % $input
Shantanu Pavgi wrote:
>
> On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote:
>
> > Shantanu Pavgi wrote:
> >>
> >> Hi,
> >>
> >> There is a 'set_metadata_externally' setting in universe_wsgi.ini file.
> >> What is involved
ouise-Amélie Schmitt a écrit :
> >Thanks a lot!
> >
> >I found another way to do it but it is awfully more complicated so
> >I'll change as soon as I have some time.
> >
> >Best,
> >L-A
> >
> >
> >Le 23/08/2011 19:49, Nate Coraor
Shantanu Pavgi wrote:
>
> Hi,
>
> There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What
> is involved in this step? Is it run for every dataset/output being generated
> in the galaxy?
Hi Shantanu,
Metadata is always detected/set on all job outputs. This setting simpl
post this with
> IGV support.
Hi Iry,
If you get anything back from the IGV folks please post a followup.
Since IGV runs in the local JVM, that it works with one browser and not
another on the same system doesn't make a lot of sense.
--nate
>
> Thanks,
> Iry
>
>
> On 8
use C code. Could you try scrambling pysam as instructed below and see
what the results are? You will have to do this for each egg that can't
be downloaded.
--nate
>
> On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor wrote:
>
> > Paul Tanger wrote:
> > > That worked,
you get from:
python ./scripts/get_platforms.py
? Note that this needs to have the path changed from append to insert
as in the previous scripts.
Thanks,
--nate
>
> On Mon, Aug 29, 2011 at 10:51 AM, Nate Coraor wrote:
>
> > Paul Tanger wrote:
> > >
Louise-Amélie Schmitt wrote:
> Le 29/08/2011 15:52, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>Hello everyone,
> >>
> >>These questions are a bit silly but I'm really ignorant when it
> >>comes to security. Sorry about that.
> >
s_requirement(), ), env,
> egg.fetch )
> File "/Users/paultanger/galaxy-dist/lib/pkg_resources.py", line 565, in
> resolve
> raise DistributionNotFound(req) # XXX put more info here
> pkg_resources.DistributionNotFound: numpy==1.6.0
> Fetch failed.
It could be a con
does this have an
effect?
--nate
>
> pkg_resources is:
> '/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6/site-packages/pkg_resources.py'>
>
>
>
> On Mon, Aug 29, 2011 at 8:17 AM, Paul Tanger wrote:
>
> > It is free for acad
Louise-Amélie Schmitt wrote:
> Hi,
>
> I ran into a little something that is a bit annoying for debug when
> trying to upload files through the API with
> library_upload_from_import_dir.py. When the specified folder is
> wrong, python tries to process the error tuple like a dict, so the
> original
Crystal Goh wrote:
>
> Dear Nate,
>
> Thanks.
>
> I used multiple account as I have several csfasta and qual files and each
> file is large in size.
>
> My account is gohweip...@hotmail.com.
> Can I get increement for disk quota for this account so that I can used only
> 1 account that can
rces and see which version it's using.
--nate
>
> On Fri, Aug 26, 2011 at 12:43 PM, Nate Coraor wrote:
>
> > Paul Tanger wrote:
> > > Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought)
> > python
> > > 2.6 (EPD version 6.1-1)? I get
It's looking like tomorrow or Wednesday at this point. We're working on
the new feature documentation and news brief right now.
--nate
Glen Beane wrote:
> Bump!
>
> We want to upgrade to get some of the newer features (since we skipped the
> last dist update), but we don't want to upgrade now
Louise-Amélie Schmitt wrote:
> Hello everyone,
>
> These questions are a bit silly but I'm really ignorant when it
> comes to security. Sorry about that.
>
> Why use API keys instead of user names? Is it to to prevent anyone
> from figuring out who is behind an URL? Or did I miss the point?
Hi
Jack Zhu wrote:
> Hi all,
>
> I have problems with updating my local instance of Galaxy.
> Specifically I can not migrate the database schema from 80 to 81:
Hi Jack,
Thanks for reporting this issue. It has been fixed in changeset
5951:62d51750d7df.
--nate
>
> --
> $$ sh manage_db
Zhibin Lu wrote:
> Hello,
>
> When i try to upload bam files into galaxy data library though
> system paths with "link to files without copying into galaxy"
> option, galaxy always complains that
>
> "The uploaded files need grooming, so change your*Copy data into
> Galaxy?*selection to be*Copy f
Chorny, Ilya wrote:
> I noticed that when uploading multiple files only one job gets submitted to
> the queue. Is there a way for galaxy to split that up on multiple nodes?
Not at present, no. Which upload method are you using? This is
probably something that could be done for certain types (li
Hi Iry,
By default, PasteScript is looking for a section named [server:main].
With this config, you can start the servers with:
% sh run.sh --server-name=web0
% sh run.sh --server-name=web1
% sh run.sh --server-name=web2
--nate
Iry Witham wrote:
> I have performed a new install of
Holger Klein wrote:
> Dear all,
>
> I'd like to integrate external user authentication with our local galaxy
> installation. So far we are running nginx as proxy, but all examples I
> found for LDAP and galaxy are for apache. Is anybody out there who has a
> working installation with LDAP and ngin
Duddy, John wrote:
> Interesting - this was a workflow with exactly 1 step - the "add a column"
> tool. I looked in my database/files/000 directory, and there was no dataset
> id 53 - would that be an id in the history_dataset_association table?
Yeah, that's the hda id. The files are named with
Edward Kirton wrote:
> i thought i recalled reading about downloading files from a history
> via ftp, but i could been mistaken -- couldn't find anything on the
> wiki or mailing list archives. does this feature exist?
>
> what's the best way for users to download many or large files other
> than
Crystal Goh wrote:
>
> Hi, I am Crystal.
>
> As Tophat for SOLiD only available in Galaxy Test (not available in Galaxy
> Main), I uploaded my csfasta and qual files to Galaxy Test. As the file size
> very big, the disk space used up is 13.5Gb and I cannot use any tool. This
> means after upl
Paul Tanger wrote:
> Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python
> 2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the
> fact that I have EPD python, not the generic python that was preinstalled?
> Any ideas?
>
> Thanks!
>
> Some eggs are
Chorny, Ilya wrote:
> I get these two error in the log file. The job finishes correctly and a
> metadata file is created but I still get the error. Can anyone provide me
> with more detail about what this error means? The second error is incorrect
> because the files were deleted.
>
>
> settin
Hi Ilya,
Sorry, I haven't yet had a chance to check out your code. Are you using
the username column of the user table to determine the local username?
This would then be job.user.username.
--nate
Chorny, Ilya wrote:
> So I figured out that it is job/runners/__init__.py that does the cleanup.
dhivya arasappan wrote:
> Hi,
>
> We have a local instance of galaxy at our institution. I've been
> trying to use several existing wrappers for tools on galaxy right
> now, for example, bwa_wrapper, cufflinks_wrapper to run bwa,
> cufflinks through galaxy. I keep seeing the following error:
>
Edward Kirton wrote:
> also, delete and purge a quota seems to have no effect.
Hi Ed,
They work for me. Note that delete/purge do not actually delete the db
row itself.
Delete marks the quota as deleted, and it no longer counts against any
associated users. Purge removes all of the user/group
Edward Kirton wrote:
> i created some quotas which were assigned to groups (set as for "yes,
> registered users") but apparently the groups didn't initially stick; i had
> to edit the quota after creation to reassign the group.
Hi Ed,
The default quota for a class of users (registered or unregist
You can also use the 'upload_store_access' option to the nginx upload
module to make the files readable:
http://www.grid.net.ru/nginx/upload.en.html
--nate
Kanwei Li wrote:
> Hi Joern,
>
> Would it be easier to just chmod the directories to reflect the new user?
>
> -K
>
> On Wed, Aug 24,
Woozy wrote:
> Hello,
>
> I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I
> import a package I've installed called PypeR. My tool works fine from the
> command line, but when I try to run it on my Amazon instance, it gives me
> this error:
>
> Traceback (most recent call l
Joseph Hargitai wrote:
>
> Hi,
>
> built a new server today to test a few things.
>
> a, Help is not clickable via Apache2 proxy
>
> 2, when you use an apache2 proxy is it for granted that local authentication
> cannot be used? I tired
> remote-user = False
>
> hoping i can use load-balancing
shashi shekhar wrote:
> Hi,
>
> I have local instance of Galaxy and i am doing some modification in
> Galaxy .So i need tool id id in local.py file . How i will get this
> information in runner file (local.py).
Hi Shashi,
Anywhere you have the job_wrapper object, the Job ID can be accessed
sohk...@notes.cc.sunysb.edu wrote:
> Hi,
> I have the production Galaxy setup and running on Mac OS Leopard 10.6,
> with postgres and apache. However, I am unable to run it as daemon. I
> don't get an error, the browser just hangs there.
> Thanks for any advice.
Hi Sohail,
How are you startin
Camille Stephan wrote:
> Hello,
>
> I just installed postgres in my machine and things seem to work fine except
> for the "Upload files from filesystems paths" option which gives the
> following error:
>
> "Invalid paths:
> /path/to/file.fasta
> "
>
> The path is correct and I tried with differe
Louise-Amélie Schmitt wrote:
> Hi,
>
> I would need to make a tool that can get the API dataset id out of
> the input dataset of the tool, how can I do that?
Hi L-A,
Pass in as an argument:
$__app__.security.encode_id( 'file.%s' % $input1.id )
Where 'input1' is the param name of your input
Chorny, Ilya wrote:
> When I run galaxy as the actual user using the code I committed to my fork, I
> run into a problem with dataset_*.dat files that have associated data wherein
> the associated data files are copied from the job_working_directory into the
> files directory. That directory is
l
it's well along.
--nate
>
> Regards
> On Aug 22, 2011, at 11:57 AM, Nate Coraor wrote:
>
> > Dave Walton wrote:
> >> Dear Galaxy developers,
> >>
> >> Our institution is trying solve our storage problem (we need lots,
> >> especially for
Chorny, Ilya wrote:
> The ftp upload module fails when a file has a comma in the file name for
> example test.bam works but when copied to test,test.bam that file fails.
Hi Ilya,
Thanks for letting us know. This has been fixed in 5921:94688ff06248.
--nate
>
> Cheers,
>
> Ilya
>
>
> Ilya C
Tanguy LE CARROUR wrote:
> Dear Nate!
>
> On Wed, 2010-09-01 at 17:21 +0200, Tanguy Le Carrour wrote:
> > On Wed, 2010-09-01 at 11:14 -0400, Nate Coraor wrote:
> > > This would be a great case for use of the (experimental) API. Set
> > > 'enable_api = True&
Dave Walton wrote:
> Dear Galaxy developers,
>
> Our institution is trying solve our storage problem (we need lots,
> especially for NGS data, and someone needs to fund it). What we would like
> to be able to do, is based on some criteria control in what location a file
> gets written to disk.
>
Sridhar A Malkaram wrote:
> Hi,
>
> I was wondering if there is a method of updating datasets in a data library,
> which was created using the option, "Upload files from filesystem paths" and
> selecting "Link to files without copying into Galaxy".
> An update operation should reflect any changes
Assaf Gordon wrote:
> Hi Colin,
>
> colin molter wrote, On 08/05/2011 01:54 PM:
> > Is there a way to directly move/copy data from your galaxy history to a
> > given location in the filesystem of the same galaxy server?
> > Said differently, there is a nice way to import data from the server to
Christoph Ruttkies wrote:
> Dear Galaxy-Dev Team,
>
> I have a problem concerning the integration of galaxy into a cluster
> environment. Galaxy is installed on a server that has access to the
> local cluster network and is configured as a submit host for the Sun
> Grid Engine running on the clust
Peter Cock wrote:
> On Fri, Jul 29, 2011 at 5:09 PM, Duddy, John wrote:
> > We had similar problems on NFS mounts to Isilon. We traced it to
> > the default timeout for attribute caching on NFS mounts, which
> > does not force a re-read of directory contents (hence file existence
> > or size) for
shashi shekhar wrote:
> Hi
>
>
> In my galaxy instance, whatever jobs i am submitting it goes into queued
> state.
> If I restart the server then the previous submitted jobs state changes to
> running. but the newly submitted jobs again goes to queued state.
>
> I am at a loss to understand thi
liyanhui607 wrote:
> Dear Sir,
>
> We have a program writen in perl. It can run nomally in linux
> environment with a file saved as result.
>
>After added it to galaxy system, we found that it can produce the
> right result file in directary "/var/we/galaxy-dist/database/fi
> ICS - Bioinformatics Engineer
> J. Craig Venter Institute
> 301-795-7743
> -------
>
> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu]
> Sent: Wednesday, August 17, 2011 12:52 PM
> To: Sanka, Ravi
>
shashi shekhar wrote:
> Hi ALL,
>
> I want to delete some data from history_dataset_association. Will it
> effect any other tables.and I want to delete records for last 3 days by
> sqlite query manually.How may tables will be effected by this and provide me
> tables name .How can i delete the r
Peter Cock wrote:
> On Wed, Jul 27, 2011 at 9:06 AM, Peter Cock wrote:
> > On Tue, Jul 26, 2011 at 8:16 PM, Luobin Yang wrote:
> >> I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
> >> 1. use local /tmp for temporary files
> >> 2. use the network shared /home/galaxy/galaxy-dist/d
Roman Valls wrote:
> Hey Nate,
>
>
> On 2011-08-16 20:21, Nate Coraor wrote:
> > Roman Valls wrote:
> >> Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
> >>
> >> I wonder how this approach will work out when one runs g
Joseph Hargitai wrote:
>
> Hi,
>
> is there a best practices, to replace general SGE requests with requests
> specific to applications -
Hi Joe,
I've moved this question to the dev list since it concerns a local
installation. You can tailor SGE options per-tool as shown at the
bottom of the p
Sanka, Ravi wrote:
> Hello,
>
> We have recently put a local installation of Galaxy on our network and
> connected it to a MYSQL database. In order to have more space available for
> uploaded and created files, we also changed the values of file_path and
> new_file_path in the config file. The
michael burrell (TSL) wrote:
> Good afternoon
>
> I am having some trouble updating our local galaxy, in summary it seems to
> fail. I have included the errors below and would really appreciate any
> assistance that could be offered.
>
> galaxy@jic55119:~/software/galaxy-ceneral$ sh manage_db.s
David Hoover wrote:
> We've run into an error with the SAM to BAM converter.
>
> An error occurred running this job: Samtools Version: 0.1.15 (r949:203)
> Error extracting alignments from
> (/gs1/users/galaxy/pro/database/files/000/dataset_285.dat), requested number
> of bytes is more than a Pyt
incremented the
database version. If you still have the database we could double check,
although it may not be possible to determine how it happened regardless.
--nate
>
> Thanks
>
> Michael.
>
> On 16/08/2011 20:05, "Nate Coraor" wrote:
>
> >michael burrell (T
Luobin Yang wrote:
> Hi, Nate,
>
> Yeah, I've already solved the issue, basically used the -e parameter as you
> mentioned here. I think the documentation should be corrected.
Thanks, I've fixed the documentation.
>
> Thanks,
> Luobin
>
> On Tue, Aug 16,
Luobin Yang wrote:
> Hi, Nate,
>
> On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor wrote:
>
> > Hi Luobin,
> >
> > Sorry for the delay in response. I would suggest moving this discussion
> > to the galaxy-dev mailing list since it does not contain any pri
michael burrell (TSL) wrote:
> Good Morning,
>
> I am getting a big problem with our production server when I upgrade to the
> latest change set (it was quite out of date). I have attached quite a long
> paster output to try and show whats going on,
>
> Our galaxy instance no longer seems to ru
Luobin Yang wrote:
> Hi,
>
> I am trying to scramble the pbs_python egg for my galaxy installation, when
> I execute the following command:
>
> "LIBTORQUE_DIR=/usr/local/lib python scripts/scramble.py pbs_python"
>
> I got lots messages like the following:
>
> scramble(): Egg already exists, re
Roman Valls wrote:
> Thanks indeed for the ~/.slurm_drmaa.conf hint Mariusz, very useful !
>
> I wonder how this approach will work out when one runs galaxy as advised
> in a production setting:
>
> http://usegalaxy.org/production
>
> Together with the gordon patch to run drmaa as different user
W. Augustine Dunn III wrote:
> I am starting to really get the hang of customizing my new galaxy instance,
> and please just let me THANK YOU GUYS!
>
> However, I am also running into a problem. I am trying to link genome fasta
> files that i obtained through metazoa.ensembl.org. I created a lib
ky
>
> > Hi Nate,
> >
> > No, our Galaxy server is not behind Apache. Our Galaxy is configured as it
> > is can be used only by registered users, not anonymous. If I disable
> > require_login in universe_wsgi.ini file then displaying of tracks in our
> &
ctly via the port of its built-in web server
(by default, 8080), and request to display a dataset, does it set the
X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the
underlying disk file, do you get an error message from nginx or from
Galaxy?
Name of server to connect to via SFTP.
Then restart Galaxy.
--nate
>
> Thank you once again.
> Regards
> Somy.
>
>
> On Mon, Jun 13, 2011 at 10:57 PM, Nate Coraor wrote:
>
> > somy ork wrote:
> > > Hi,
> > >
> > > Am trying to configur
Peter Cock wrote:
> On Fri, Jun 3, 2011 at 10:03 AM, Peter Cock wrote:
> > Thanks for the link - I was aware my initial work on adding a generic
> > XML filetype was missing some steps, but I ran out of time yesterday:
> > https://bitbucket.org/galaxy/galaxy-central/issue/568
>
> Hi all,
>
> Cou
Iry Witham wrote:
> Hi Everyone,
>
> I have been tasked with getting the IGV working within our Galaxy
> instance. I have modified our Nginx configuration based on the more advanced
> configuration under "Sending files using nginx" on the nginxProxy page in the
> wiki. The IGV viewer comp
Andrew Warren wrote:
> So would the current correct method for setting up multi-threaded jobs on a
> cluster be to specify custom runners in the [galaxy:tool_runners] section of
> the universe config file for EVERY tool that uses a multiple threads
> (assuming the default is set to one)?
>
> For e
d total_size will be greater if this is the case.
> Although 'allow_user_dataset_purge' setting seems to be very usefull, but it
> is absent in my universe_wsgi.ini file (galaxy_dist).
Have a look in the universe_wsgi.ini.sample file for it.
--nate
>
>
>
> 06.0
Joseph Hargitai wrote:
>
> > 2,
> > switched from SQLlite to postgres and have this strange double login issue.
> > Included image - need to login twice and logout twice. Double tab -
>
> By any chance, are you using require_login = True in the config? Which
> logout link are you clicking to ge
Sergei Ryazansky wrote:
> Hello all,
>
> we have the UCSC genome browser mirror as well as Galaxy mirror. The
> Galaxy has a feature enabling a user to display the data at UCSC genome
> browser as custom tracks. I have configured the galaxy to display the data
> to our UCSC browser mirror but it d
Assaf Gordon wrote:
> Hello Sergei,
>
> I'm experimenting with the clean-up scripts myself, so perhaps I can offer
> some information (the galaxy team is welcomed to correct me and/or explain
> better).
>
>
> 1. If you look at the output of your query, you'll notice that the "purged"
> field
Joseph Hargitai wrote:
>
> Hi,
>
> 1,
> referencing old thread:
> http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html
>
> is the delete functionality still status-quo? i.e - there is no delete other
> than the workaround?
Hi Joe,
Since this is regarding a local installation, I've
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